well this is what i think i could be wrong. the covenant holds the forerunners as their "gods" and most probably their creators the covenant prophets/priests have taught them this for centuries but they have found out something about the forerunners that would literally destroy their power and control over their own people... the forerunners are HUMAN and if the normal covenant races find out all they have been taught would have been a fake a lie and would surely cause havoc against their own races but most importantly the priests themselves. that's why they have ordered the complete genocide of all the human race in order to silence the real truth that one day would eventually be found if their plans are not carried out.

So, Humans are either related to the Forerunner directly, or have had a special relationship with them in the past.

But surely the Elites and Prophets have built their covenant upon a foundation of trust, where they share everything. Why, if word of this plot was to get out...